In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which are crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics technologies provide unprecedented opportunities to systematically infer and analyze CCC from these omics data, either by integrating prior knowledge of ligand-receptor interactions (LRIs) or through de novo approaches. A variety of computational methods have been developed, focusing on methodological innovations, accurate modeling of complex signaling mechanisms, and investigation of broader biological questions. These advances have greatly enhanced our ability to analyze CCC and generate biological hypotheses. Here, we introduce the biological mechanisms and modeling strategies of CCC, and provide a focused overview of more than 140 computational methods for inferring CCC from single-cell and spatial transcriptomic data, emphasizing the diversity in methodological frameworks and biological questions. Finally, we discuss the current challenges and future opportunities in this rapidly evolving field.

Spatial transcriptomics enables gene expression profiling with spatial context, offering unprecedented insights into the tissue microenvironment. However, most computational models treat genes as isolated numerical features, ignoring the rich biological semantics encoded in their symbols. This prevents a truly deep understanding of critical biological characteristics. To overcome this limitation, we present SemST, a semantic-guided deep learning framework for spatial transcriptomics data clustering. SemST leverages Large Language Models (LLMs) to enable genes to "speak" through their symbolic meanings, transforming gene sets within each tissue spot into biologically informed embeddings. These embeddings are then fused with the spatial neighborhood relationships captured by Graph Neural Networks (GNNs), achieving a coherent integration of biological function and spatial structure. We further introduce the Fine-grained Semantic Modulation (FSM) module to optimally exploit these biological priors. The FSM module learns spot-specific affine transformations that empower the semantic embeddings to perform an element-wise calibration of the spatial features, thus dynamically injecting high-order biological knowledge into the spatial context. Extensive experiments on public spatial transcriptomics datasets show that SemST achieves state-of-the-art clustering performance. Crucially, the FSM module exhibits plug-and-play versatility, consistently improving the performance when integrated into other baseline methods.

Inconsistencies between clinical and omics data may arise within medical cohorts. The identification, annotation and explanation of anomalous omics-based patients or individuals may become crucial to better reshape the disease, e.g., by detecting early onsets signaled by the omics and undetectable from observable symptoms. Here, we developed MLASDO (Machine Learning based Anomalous Sample Detection on Omics), a new method and software tool to identify, characterize and automatically describe anomalous samples based on omics data. Its workflow is based on three steps: (1) classification of healthy and cases individuals using a support vector machine algorithm; (2) detection of anomalous samples within groups; (3) explanation of anomalous individuals based on clinical data and expert knowledge. We showcase MLASDO using transcriptomics data of 317 healthy controls (HC) and 465 Parkinson's disease (PD) cases from the Parkinson's Progression Markers Initiative. In this cohort, MLASDO detected 15 anomalous HC with a PD-like transcriptomic signature and PD-like clinical features, including a lower proportion of CD4/CD8 naive T-cells and CD4 memory T-cells compared to HC (P<3.5*10^-3). MLASDO also identified 22 anomalous PD cases with a transcriptomic signature more similar to that of HC and some clinical features more similar to HC, including a lower proportion of mature neutrophils compared to PD cases (P<6*10^-3). In summary, MLASDO is a powerful tool that can help the clinician to detect and explain anomalous HC and cases of interest to be followed up. MLASDO is an open-source R package available at: https://github.com/JoseAdrian3/MLASDO.

Histopathology and transcriptomics are fundamental modalities in oncology, encapsulating the morphological and molecular aspects of the disease. Multi-modal self-supervised learning has demonstrated remarkable potential in learning pathological representations by integrating diverse data sources. Conventional multi-modal integration methods primarily emphasize modality alignment, while paying insufficient attention to retaining the modality-specific structures. However, unlike conventional scenarios where multi-modal inputs share highly overlapping features, histopathology and transcriptomics exhibit pronounced heterogeneity, offering orthogonal yet complementary insights. Histopathology provides morphological and spatial context, elucidating tissue architecture and cellular topology, whereas transcriptomics delineates molecular signatures through gene expression patterns. This inherent disparity introduces a major challenge in aligning them while maintaining modality-specific fidelity. To address these challenges, we present MIRROR, a novel multi-modal representation learning method designed to foster both modality alignment and retention. MIRROR employs dedicated encoders to extract comprehensive features for each modality, which is further complemented by a modality alignment module to achieve seamless integration between phenotype patterns and molecular profiles. Furthermore, a modality retention module safeguards unique attributes from each modality, while a style clustering module mitigates redundancy and enhances disease-relevant information by modeling and aligning consistent pathological signatures within a clustering space. Extensive evaluations on TCGA cohorts for cancer subtyping and survival analysis highlight MIRROR's superior performance, demonstrating its effectiveness in constructing comprehensive oncological feature representations and benefiting the cancer diagnosis.

Emerging research has highlighted that artificial intelligence based multimodal fusion of digital pathology and transcriptomic features can improve cancer diagnosis (grading/subtyping) and prognosis (survival risk) prediction. However, such direct fusion for joint decision is impractical in real clinical settings, where histopathology is still the gold standard for diagnosis and transcriptomic tests are rarely requested, at least in the public healthcare system. With our novel diffusion based crossmodal generative AI model PathGen, we show that genomic expressions synthesized from digital histopathology jointly predicts cancer grading and patient survival risk with high accuracy (state-of-the-art performance), certainty (through conformal coverage guarantee) and interpretability (through distributed attention maps).

The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and spatial omics data remains challenging. First, single-cell sequencing data are high-dimensional and sparse, often contaminated by noise and uncertainty, obscuring the underlying biological signals. Second, these data often encompass multiple modalities, including gene expression, epigenetic modifications, and spatial locations. Integrating these diverse data modalities is crucial for enhancing prediction accuracy and biological interpretability. Third, while the scale of single-cell sequencing has expanded to millions of cells, high-quality annotated datasets are still limited. Fourth, the complex correlations of biological tissues make it difficult to accurately reconstruct cellular states and spatial contexts. Traditional feature engineering-based analysis methods struggle to deal with the various challenges presented by intricate biological networks. Deep learning has emerged as a powerful tool capable of handling high-dimensional complex data and automatically identifying meaningful patterns, offering significant promise in addressing these challenges. This review systematically analyzes these challenges and discusses related deep learning approaches. Moreover, we have curated 21 datasets from 9 benchmarks, encompassing 58 computational methods, and evaluated their performance on the respective modeling tasks. Finally, we highlight three areas for future development from a technical, dataset, and application perspective. This work will serve as a valuable resource for understanding how deep learning can be effectively utilized in single-cell and spatial transcriptomics analyses, while inspiring novel approaches to address emerging challenges.

The task of spatial clustering of transcriptomics data is of paramount importance. It enables the classification of tissue samples into diverse subpopulations of cells, which, in turn, facilitates the analysis of the biological functions of clusters, tissue reconstruction, and cell-cell interactions. Many approaches leverage gene expressions, spatial locations, and histological images to detect spatial domains; however, Graph Neural Networks (GNNs) as state of the art models suffer from a limitation in the assumption of pairwise connections between nodes. In the case of domain detection in spatial transcriptomics, some cells are found to be not directly related. Still, they are grouped as the same domain, which shows the incapability of GNNs for capturing implicit connections among the cells. While graph edges connect only two nodes, hyperedges connect an arbitrary number of nodes along their edges, which lets Hypergraph Neural Networks (HGNNs) capture and utilize richer and more complex structural information than traditional GNNs. We use autoencoders to address the limitation of not having the actual labels, which are well-suited for unsupervised learning. Our model has demonstrated exceptional performance, achieving the highest iLISI score of 1.843 compared to other methods. This score indicates the greatest diversity of cell types identified by our method. Furthermore, our model outperforms other methods in downstream clustering, achieving the highest ARI values of 0.51 and Leiden score of 0.60.

Single-cell multi-omics (scMulti-omics) refers to the paired multimodal data, such as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), where the regulation of each cell was measured from different modalities, i.e. genes and proteins. scMulti-omics can reveal heterogeneity inside tumors and understand the distinct genetic properties of diverse cell types, which is crucial to targeted therapy. Currently, deep learning methods based on attention structures in the bioinformatics area face two challenges. The first challenge is the vast number of genes in a single cell. Traditional attention-based modules struggled to effectively leverage all gene information due to their limited capacity for long-context learning and high-complexity computing. The second challenge is that genes in the human genome are ordered and influence each other's expression. Most of the methods ignored this sequential information. The recently introduced Test-Time Training (TTT) layer is a novel sequence modeling approach, particularly suitable for handling long contexts like genomics data because TTT layer is a linear complexity sequence modeling structure and is better suited to data with sequential relationships. In this paper, we propose scFusionTTT, a novel method for Single-Cell multimodal omics Fusion with TTT-based masked autoencoder. Of note, we combine the order information of genes and proteins in the human genome with the TTT layer, fuse multimodal omics, and enhance unimodal omics analysis. Finally, the model employs a three-stage training strategy, which yielded the best performance across most metrics in four multimodal omics datasets and four unimodal omics datasets, demonstrating the superior performance of our model. The dataset and code will be available on https://github.com/DM0815/scFusionTTT.

With the rapid advancement of Spatial Resolved Transcriptomics (SRT) technology, it is now possible to comprehensively measure gene transcription while preserving the spatial context of tissues. Spatial domain identification and gene denoising are key objectives in SRT data analysis. We propose a Contrastively Augmented Masked Graph Autoencoder (STMGAC) to learn low-dimensional latent representations for domain identification. In the latent space, persistent signals for representations are obtained through self-distillation to guide self-supervised matching. At the same time, positive and negative anchor pairs are constructed using triplet learning to augment the discriminative ability. We evaluated the performance of STMGAC on five datasets, achieving results superior to those of existing baseline methods. All code and public datasets used in this paper are available at https://github.com/wenwenmin/STMGAC and https://zenodo.org/records/13253801.

Multi-modal learning that combines pathological images with genomic data has significantly enhanced the accuracy of survival prediction. Nevertheless, existing methods have not fully utilized the inherent hierarchical structure within both whole slide images (WSIs) and transcriptomic data, from which better intra-modal representations and inter-modal integration could be derived. Moreover, many existing studies attempt to improve multi-modal representations through attention mechanisms, which inevitably lead to high complexity when processing high-dimensional WSIs and transcriptomic data. Recently, a structured state space model named Mamba emerged as a promising approach for its superior performance in modeling long sequences with low complexity. In this study, we propose Mamba with multi-grained multi-modal interaction (SurvMamba) for survival prediction. SurvMamba is implemented with a Hierarchical Interaction Mamba (HIM) module that facilitates efficient intra-modal interactions at different granularities, thereby capturing more detailed local features as well as rich global representations. In addition, an Interaction Fusion Mamba (IFM) module is used for cascaded inter-modal interactive fusion, yielding more comprehensive features for survival prediction. Comprehensive evaluations on five TCGA datasets demonstrate that SurvMamba outperforms other existing methods in terms of performance and computational cost.